UJAC is a collection of Java components that may be useful for your project. It provides a powerful expression interpreter, a iText based document processing engine that generates PDF documents based on XML templates, a charting library and much more.
CaLi2CoPi is a multiplatform PDF parser library programmed in PostScript. Works with several specialized switch in order to verify, add, extract or change any PDF content. Also supports online execution on web based user interface via Ghostscript.
Research Description Language (RDL) is an XML application for describing and publishing scientific research efforts. Research Editor (REd) is a tool for editing RDL documents, and exporting them to LaTeX, PDF, etc.